Methods and compositions for diagnosis and treatment of autoimmune disease secondary to multiple sclerosis

ABSTRACT

The invention provides methods of diagnosing and treating multiple sclerosis (MS) patients, including methods of identifying and treating multiple sclerosis patients who are at increased risk of developing a secondary autoimmune disease following lymphocyte depletion, caused, e.g., by treatment with an anti-CD52 antibody. Also embraced are methods of selecting treatment regimens for MS patients, and reagents useful in the above methods.

This application is a divisional application of U.S. patent applicationSer. No. 13/123,188, filed Jun. 7, 2011 (now abandoned), which is anational stage application under 35 U.S.C. §371 of InternationalApplication PCT/M2009/007327, filed Oct. 8, 2009 (now expired), whichapplication claims priority to U.S. Provisional Application 61/195,658,filed Oct. 8, 2008 (now expired), U.S. Provisional Application61/197,187, filed Oct. 24, 2008 (now expired), and U.S. ProvisionalApplication 61/198,631, filed Nov. 7, 2008 (now expired). The contentsof the foregoing applications are hereby incorporated by reference intheir entirety.

The Sequence Listing associated with this application is being submittedelectronically via EFS-WEB in text format, and is hereby incorporated byreference into the specification. The name of the text file containingthe Sequence Listing is 001662_0019_302 Sequence_Listing.txt. The textfile is 9,001 bytes in size, and was created on Feb. 1, 2016.

BACKGROUND OF THE INVENTION

Multiple sclerosis (“MS”) is an inflammatory autoimmune disorder of thecentral nervous system (Compston and Coles, Lancet 372, 1502-17 (2008)).With a prevalence of about one in 1000, MS is the most common cause ofneurological disability in young adults (Polman and Uitdehaag, BMJ 321,490-4 (2000)). MS involves engagement of the immune system, acuteinflammatory injury of axons and glia, recovery of function andstructural repair, post-inflammatory gliosis, and neurodegeneration(see, e.g., Compston and Coles, 2008). These sequential processesunderlie a clinical course characterized by episodes with recovery,episodes leaving persistent deficits, and secondary progression. Id.

The goal of MS treatment is to reduce the frequency and severity ofrelapses, prevent disability arising from disease progression, andpromote tissue repair (Compston and Coles, 2008). The primary approachto MS treatment is modulation or suppression of the immune system.Currently available MS drugs include interferon beta-1a (e.g., AVONEXand REBIF), interferon beta-1b (e.g., BETASERON), glatiramer acetate(e.g., COPAXONE), mitoxantrone (e.g., NOVANTRONE), and natalizumab(e.g., TYSABRI). Another promising new drug for MS is alemtuzumab(CAMPATH-1H).

Alemtuzumab is a humanized monoclonal antibody directed against CD52, aprotein widely distributed on the surface of lymphocytes and monocytesbut with unknown function. Alemtuzumab has been used to treat B-cellchronic lymphocytic leukaemia. A single pulse of treatment leads to arapid, profound, and prolonged lymphopenia. Cell numbers recover but atvarying rates; CD4+ T cells are particularly slow to recover, remainingdepleted for at least five years (Coles et al., Journal of Neurology253, 98-108 (2006)). A phase 2 trial (CAMMS-223 study group; Coles etal., N. Engl. J. Med. 359, 1786-1801 (2008)) has shown that alemtuzumabis highly effective in treating early relapsing-remitting multiplesclerosis. This drug reduces the risk of disease activity andaccumulation of disability by over 70% compared to interferon-beta inpatients with early relapsing-remitting multiple sclerosis. Theprincipal adverse effect is autoimmunity, arising in the setting of Tcell lymphopenia months to years after dosing. About 20%-30% of patientsdevelop thyroid autoimmunity, mainly Graves' disease (Coles et al.,Lancet 354, 1691-1695 (1999)), and 3% have immune thrombocytopenia (ITP)(Coles et al., 2008). Single cases of Goodpasture's disease, autoimmuneneutropenia (Coles et al., Journal of Neurology 253, 98-108 (2006)), andautoimmune haemolytic anaemia (unpublished observation) also have beenobserved. In addition, a further 5.5% of patients develop sustainednon-thyroid autoantibodies without clinical disease (Coles et al.,2006). The timing and spectrum of autoimmunity after alemtuzumab issimilar to that seen in other examples of “reconstitution autoimmunity”in other clinical contexts; for example, autoimmune thyroid disease andautoimmune cytopenias also predominate months to years afterhematopoietic stem cell transplantation or antiretroviral treatment ofHIV (Chen et al., Medicine (Baltimore) 84, 98-106 (2005); Daikeler andTyndall, Best. Pract. Res. Clin. Haematol. 20, 349-360 (2007); Jubaultet al., J. Clin. Endocrinol. Metab. 85, 4254-4257 (2000); Ting, Ziegler,and Vowels, Bone Marrow Transplant. 21, 841-843 (1998); Zandman-Goddardand Shoenfeld, Autoimmun. Rev. 1, 329-337 (2002)).

While autoimmunity arising in the context of lymphopenia is wellrecognized in animal models, it is rarely encountered and, hence,difficult to study in humans. Most lymphopenic subjects do not developautoimmunity, suggesting that additional factors are involved (Krupicaet al., Clin Immunol 120, 121-128 (2006)). It remains unclear what thoseadditional factors are. Depletion of T regulatory cells has beenconsidered as one factor, as seen in the murine colitis and gastritismodels (Alderuccio et al., J Exp. Med 178, 419-426 (1993); McHugh etal., J. Immunol 168, 5979-5983 (2002); Powrie et al., Int. Immunol 5,1461-1471 (1993); Sakaguchi et al., J Immunol 155, 1151-1164 (1995)).However, it has been observed that T regulatory cells are increasedafter alemtuzumab in human patients and thereafter return to normallevels (Cox et al., Eur J Immunol 35, 3332-3342 (2005)). Thisobservation has since been replicated (Bloom et al., Am J Transplant. 8,793-802 (2008)) and is in keeping with other experimental lymphopenicmodels (de Kleer, I. et al., Blood 107, 1696-1702 (2006); Zhang, H. etal., Nat Med 11, 1238-1243 (2005)).

SUMMARY OF THE INVENTION

We have invented new and useful methods and compositions for improvingrisk management in MS treatment. The methods and compositions reduce MStreatment side effects such as secondary autoimmunity, and help healthcare providers and patients in selecting regimens for MS treatment andpost-treatment monitoring. The methods and compositions of thisinvention are based on our discovery that in multiple sclerosis (MS)patients, elevated IL-21, detectable even before lymphocyte depletingtherapy such as alemtuzumab therapy, correlates with increased risk ofdeveloping secondary autoimmunity after the therapy. We have furtherdiscovered that an individual's IL-21 level may be geneticallydetermined: single nucleotide polymorphisms (SNP) genotypes of A/A atSNP rs13151961, G/G at SNP rs6822844, and C/C at SNP rs6840978 areassociated with elevated IL-21.

Accordingly, the present invention provides methods for identifying anMS patient who has elevated interleukin-21 (IL-21) compared to IL-21 ina subject without an autoimmune disease. In some embodiments, themethods comprise the step of measuring IL-21 in a blood sample from theMS patient, thereby identifying an MS patient having elevated IL-21compared to said subject. Alternatively, the methods comprise the stepof genotyping the patient to detect the presence or absence in thepatient of one or more genotypes of single nucleotide polymorphisms(SNPs) associated with elevated IL-21 such as those selected from thegroup consisting of: A/A at SNP rs13151961, G/G at SNP rs6822844, andC/C at SNP rs6840978, wherein the presence of one or more of saidgenotypes is associated with elevated IL-21.

The invention further provides methods for identifying an MS patient whois at increased risk of developing a secondary autoimmune diseasefollowing lymphocyte depletion. In some embodiments, the methodscomprise the step of ascertaining (e.g., by measuring) the level ofinterleukin-21 (IL-21) in a blood sample from the MS patient, wherein anelevated IL-21 level compared to a subject without an autoimmune diseaseindicates that the patient is at increased risk of developing asecondary autoimmune disease compared to MS patients without elevatedIL-21. Alternatively, the methods comprise the step of ascertaining(e.g., by genotyping) the presence or absence in the patient of one ormore genotypes of single nucleotide polymorphisms (SNPs) associated withelevated IL-21 such as those selected from the group consisting of: A/Aat SNP rs13151961, G/G at SNP rs6822844, and C/C at SNP rs6840978,wherein the presence of one or more (e.g., two or three) of saidgenotypes is associated with an increased risk of developing a secondaryautoimmune disease compared to MS patients without said one or moregenotypes. These methods optionally comprise the step of informing thepatient and/or his/her health care provider of said increased risk,and/or the step of recording the increased risk.

The invention further provides methods for selecting or identifying anMS patient in need of heightened monitoring for development of asecondary autoimmune disease after lymphocyte depleting therapy. Thesemethods may comprise the step of measuring IL-21 in a blood sample fromthe MS patient, wherein elevated IL-21 in said patient compared to asubject without an autoimmune disease indicates that the patient is inneed of heightened monitoring for development of a secondary autoimmunedisease compared to MS patients without elevated IL-21. Alternatively,the methods may comprise the step of genotyping the patient to detectthe presence or absence of one or more genotypes of SNPs associated withelevated IL-21 such as those selected from the group consisting of: A/Aat SNP rs13151961, G/G at SNP rs6822844, and C/C at SNP rs6840978,wherein the presence of one or more of said SNPs indicates that thepatient is in need of heightened monitoring for development of asecondary autoimmune disease compared to MS patients without said one ormore genotypes. These methods optionally comprise the step of informingthe patient and/or his/her health care provider of the need forheightened monitoring, and/or the step of recording the need.

The invention also provides methods for informing a treatment for an MSpatient, comprising measuring IL-21 in a blood sample from said patientor genotyping the patient for the presence or absence of theaforementioned three SNP phenotypes, and selecting a treatment regimenappropriate for the IL-21 measurement or genotype.

The invention provides methods for treating MS in a patient known to bein need thereof, comprising the steps of (a) obtaining or ascertaininginformation on (i) IL-21 in a blood sample from the patient (e.g., bymeasuring IL-21 in the sample); or (ii) the presence or absence of oneor more genotypes of single-nucleotide polymorphisms (SNPs) associatedwith elevated IL-21 such as those selected from the group consisting of:A/A at SNP rs13151961, G/G at SNP rs6822844 G/G, and C/C at SNPrs6840978 (e.g., by genotyping the patient); (b) administering atherapeutic agent for multiple sclerosis to said patient, and (c)optionally monitoring the patient for development of a secondaryautoimmune disease. In some embodiments, the methods of treatment areused on patients who are found to have normal IL-21 levels and/or do nothave any one of the aforementioned three IL-21 SNP genotypes. Alsoembraced by the invention are anti-CD52 antibodies (e.g., alemtuzumab ora biologically similar agent), or antigen-binding portions thereof, thatare used in these treatment methods, and uses of these antibodies orantigen-binding portions in the manufacture of a medicament for use inthese treatment methods. Further embraced by the invention aretherapeutic regimens using these methods of treatment.

The invention provides methods for reducing the occurrence or severityof a secondary autoimmune disease in a multiple sclerosis patient whohas been or will be treated with a lymphocyte depleting therapy, whereinthe secondary autoimmune disease occurs after treatment with thelymphocyte depleting therapy, comprising the step of administering anIL-21 antagonist, e.g., prior to, during, or subsequent to the treatmentwith the lymphocyte depleting therapy. Also embraced by the inventionare IL-21 antagonists for use in these methods (e.g., an anti-IL-21 oranti-IL-21 receptor antibody, or an antigen-binding portion thereof; ora soluble IL-21 receptor), and uses of these IL-21 antagonists in themanufacture of a medicament for use in the methods.

The invention provides methods for assessing T cell responsiveness totreatment with a lymphocyte depleting therapy in a multiple sclerosispatient, comprising measuring caspase-3 in T cells obtained from saidpatient after said therapy, wherein an increase in caspase-3 in said Tcells compared to T cells from an MS patient not receiving said therapyis indicative of T cell responsiveness to said therapy. The measuringmay entail determining the amount or concentration of caspase-3 ornucleic acid encoding caspase-3.

The invention provides methods for informing an MS patient of anincreased risk of developing a secondary autoimmune disease followinglymphocyte depletion, comprising the steps of obtaining or ascertaininginformation on interleukin-21 (IL-21) in a blood sample from the MSpatient, wherein elevated IL-21 compared to a subject without anautoimmune disease indicates that the patient is at increased risk ofdeveloping a secondary autoimmune disease compared to MS patientswithout elevated IL-21; and informing the patient of an increased riskor lack thereof. Alternatively, the methods comprise obtaining orascertaining information on the presence or absence of one or more ofthe aforementioned IL-21 genotypes, instead of information on bloodIL-21 level. Accordingly, the invention also provides methods forinforming an MS patient of a need, or lack of a need, for heightenedmonitoring for development of a secondary autoimmune disease followinglymphocyte depleting therapy on the basis of the patient's IL-21 levelor the presence or absence of the IL-21 genotypes described above.

The invention provides methods for informing a regimen for monitoring anMS patient following lymphocyte depleting therapy, comprising the stepsof obtaining or ascertaining information on (i) IL-21 in a blood samplefrom the patient; or (ii) the presence or absence of one or moregenotypes of single-nucleotide polymorphisms (SNPs) associated withelevated IL-21 such as those selected from the group consisting of: A/Aat SNP rs13151961, G/G at SNP rs6822844 G/G, and C/C at SNP rs6840978;and selecting a monitoring regimen appropriate for the patient based onthe information. An appropriate monitoring regimen may include, forexample, measuring auto-antibodies in the patient.

The present invention provides advantages in risk management in MStreatment. For example, the invention provides methods for distributinga lymphocyte depleting drug to a patient for treating multiplesclerosis, comprising the steps of counseling the patient on theincreased risk of developing a secondary autoimmune disease followingtreatment with said drug, wherein the increased risk is associated with(i) elevated IL-21; or (ii) the presence of one or more genotypes ofsingle-nucleotide polymorphisms (SNPs) associated with elevated IL-21such as those selected from the group consisting of: A/A at SNPrs13151961, G/G at SNP rs6822844 G/G, and C/C at SNP rs6840978; andproviding the drug to the patient after said counseling, optionallyafter obtaining informed consent from the patient.

The invention further provides methods for identifying an individual whois likely to have elevated interleukin-21 (IL-21) compared to a subjectwithout any known inflammatory condition, comprising the step ofgenotyping the individual to detect the presence or absence of one ormore genotypes of single nucleotide polymorphisms (SNPs) associated withelevated IL-21 such as those selected from the group consisting of: A/Aat SNP rs13151961, G/G at SNP rs6822844, and C/C at SNP rs6840978,wherein the presence of one or more of said genotypes is associated withelevated IL-21.

In the context of this invention, lymphocyte depletion can be induced bya treatment that targets CD52, e.g., a treatment with an anti-CD52antibody (e.g., a monoclonal antibody) or an antigen-binding portionthereof. The anti-CD52 antibody can be alemtuzumab or a biologicallysimilar agent such as an antibody that competes for binding to CD52 withalemtuzumab.

In the methods of this invention, IL-21 measurement may entail measuring(e.g., detecting/quantifying) the amount or concentration of IL-21 ornucleic acid encoding IL-21 in a sample, or the amount or concentrationof mRNA encoding IL-21 in IL-21-producing cells (e.g., Th17 cells) inthe sample. In some embodiments, the measuring is of intracellularIL-21, using, for example, cytokine staining and flow cytometry. In someembodiments, the measuring is of serum IL-21, using, for example, anenzyme-linked immunosorbent assay (ELISA). Also embraced by theinvention are ELISA kits for detecting IL-21 levels in a human subject,comprising an anti-IL-21 antibody, or an antigen-binding portionthereof, or a soluble IL-21 receptor. The kits may further include aninstruction directing a user to take a blood sample from a humansubject.

In the methods of this invention, IL-21 information (includingmeasurement or genotyping) can be obtained prior to, during, orsubsequent to MS therapy. The methods of this invention can be used inthe context of any MS form, including but not limited torelapsing-remitting multiple sclerosis, primary progressive multiplesclerosis, and secondary progressive multiple sclerosis.

The invention also provides kits for treating multiple sclerosis,comprising a lymphocyte depleting therapeutic agent (e.g., an anti-CD52antibody such as alemtuzumab); and a written instruction for informing apatient or health care provider of the potential for an increased riskof developing a secondary autoimmune disease following treatment withsaid agent, wherein the increased risk is indicated by or associatedwith (i) elevated IL-21, or (ii) the presence of one or more genotypesof single-nucleotide polymorphisms (SNPs) associated with elevated IL-21such as those selected from the group consisting of: A/A at SNPrs13151961, G/G at SNP rs6822844 G/G, and C/C at SNP rs6840978.

The invention further provides kits for identifying an MS patient who isat increased risk of developing a secondary autoimmune disease followinglymphocyte depletion, comprising an anti-interleukin-21 (IL-21) antibodyand one or more reagents for detecting the binding of said antibody toIL-21 in a blood sample from the MS patient. The invention also provideskits for identifying an MS patient who is at increased risk ofdeveloping a secondary autoimmune disease following lymphocytedepletion, comprising one or more reagents suitable for identifying thegenotype of one or more single nucleotide polymorphisms (SNPs) selectedfrom the group consisting of: SNP rs13151961, SNP rs6822844, and SNPrs6840978, in a sample obtained from an individual.

Other features and advantages of the invention will be apparent from thefollowing figures and detailed description.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1A is a graph showing precursor frequency (PF) of T cells fromhealthy controls (HC), untreated patients (Pre) and at intervals of 3months post-alemtuzumab, unstimulated (Unstim), or following culturewith myelin basic protein (MBP) or thyroid stimulating hormone receptor(TSHr). (* p<0.05, ** p<0.01, *** p<0.001)

FIG. 1B is a graph showing proliferative index (PI) of T cells fromhealthy controls (HC), untreated patients (Pre) and at intervals of 3months post-alemtuzumab, unstimulated (Unstim), or following culturewith myelin basic protein (MBP) or thyroid stimulating hormone receptor(TSHr). (* p<0.05, ** p<0.01, *** p<0.001)

FIG. 1C is a graph showing the total number of viable T cells after 10days in culture from healthy controls (HC), untreated patients (Pre) andat intervals of 3 months post-alemtuzumab, unstimulated (Unstim), orfollowing culture with myelin basic protein (MBP) or thyroid stimulatinghormone receptor (TSHr). (* p<0.05, ** p<0.01, *** p<0.001)

FIG. 1D is a graph showing percentage of T cells apoptosing in responseto no stimuli or following culture with MBP or TSHr in culture fromhealthy controls (HC), untreated patients (Pre) and at intervals of 3months post-alemtuzumab. (* p<0.05, ** p<0.01, *** p<0.001)

FIG. 1E is plots and a graph showing passive T cell apoptosis fromhealthy controls and patients before and after alemtuzumab at intervalsof 3 months. (* p<0.05, ** p<0.01, *** p<0.001)

FIG. 1F is plots and a graph showing Fas-mediated T cell apoptosis fromhealthy controls and patients before and after alemtuzumab at intervalsof 3 months. (* p<0.05, ** p<0.01, *** p<0.001)

FIG. 1G is a graph showing passive CD4+ and CD8+ T cell apoptosis fromhealthy controls, pre-treatment patients and at 9 monthspost-alemtuzumab. (* p<0.05, ** p<0.01, *** p<0.001)

FIG. 1H is a graph showing Fas-mediated CD4+ and CD8+ T cell apoptosisfrom healthy controls, pretreatment patients and at 9 monthspost-alemtuzumab. (* p<0.05, ** p<0.01, *** p<0.001)

FIGS. 2A-2C are graphs showing caspase 3 mRNA expression relative tobeta-actin mRNA expression in (A) CD3+ T cells, (B) CD14+ monocytes, and(C) CD19+ B cells, respectively, either immediately ex-vivo or followingstimulation with MBP or polyclonal stimulation (anti-CD3/28 antibodies).(* p<0.05, ** p<0.01, *** p<0.001)

FIG. 3 is plots and a graph showing that autoimmunity after alemtuzumabis associated with excessive T cell apoptosis. Percentage T cellapoptosis that is passive (Un), Fas-mediated, or in response to MBP orTSHr stimulation in those without autoimmunity (Ge et al., Proceedingsof the National Academy of Sciences of the United States of America 101,3041-3046 (2004)) or those with secondary autoimmunity (Ge et al., 2004)is shown in separate plots. (* p<0.05, ** p<0.01, *** p<0.001)

FIGS. 4A and 4B are plots and graphs showing that rhIL-21 induces T cellapoptosis in vitro. They show that (A) CD4+ T cells and (B) CD8+ Tcells, respectively, unstimulated or polyclonally stimulated(anti-CD3/CD28), apoptose in response to rhIL-21 in a dose-dependentmanner. (* p<0.05, ** p<0.01, *** p<0.001)

FIGS. 5A-5D are graphs showing that rhIL-21 induces T cell proliferationin vitro. FIG. 5A is a graph showing the proliferative index ofunstimulated CD4+ and CD8+ T cells in response to rhIL-21. FIG. 5B is agraph showing the proliferative index of polyclonally stimulated(anti-CD3/CD28) CD4+ and CD8+ T cells in response to rhIL-21. FIG. 5C isa graph showing precursor frequency of unstimulated CD4+ and CD8+ Tcells in response to rhIL-21. FIG. 5D is a graph showing precursorfrequency of polyclonally stimulated CD4+ and CD8+ T cells in responseto rhIL-21. (* p<0.05, ** p<0.01, *** p<0.001)

FIG. 5E is plots showing the number of unstimulated or polyclonallystimulated (anti-CD3/CD28) CD4+ or CD8+ cells in different channels inthe absence of, or in response to, rhIL-21.

FIG. 6A is a graph showing serum IL-21 prior to and after alemtuzumabtreatment in 15 patients with, and 15 patients without, secondaryautoimmunity. (* p<0.05, ** p<0.01, *** p<0.001)

FIG. 6B is a graph showing pre-treatment serum IL-21 levels (pg/ml) inthe non-autoimmune patients (those who had no post-alemtuzumabautoimmunity) and the autoimmune patients (those who hadpost-alemtuzumab autoimmunity).

DETAILED DESCRIPTION

This invention is based on our discovery that the occurrence ofsecondary autoimmunity in an MS patient following lymphocyte depletingtherapy (e.g., after treatment with alemtuzumab) is associated withelevated IL-21 in the patient. We have discovered that IL-21 is elevatedcompared to the norm (see discussions below) even before the therapy inMS patients who later develop post-therapy secondary autoimmunity. Wealso have discovered that after lymphocyte depleting therapy, IL-21 iselevated even more dramatically in those same patients, as compared toMS patients with no signs of secondary autoimmunity, whose IL-21 iselevated to a much smaller extent. Thus, IL-21 levels are predictive ofthe occurrence of secondary autoimmunity after lymphocyte depletingtherapy in an MS patient. We also have discovered that single nucleotidepolymorphism (SNP) genotypes of A/A at SNP rs13151961, G/G at SNPrs6822844, and C/C at SNP rs6840978 are associated with elevated IL-21in an individual; thus genotyping an MS patient for the presence orabsence of these specific SNP genotypes also helps predict the risk fordeveloping secondary autoimmunity in the patient following lymphocytedepletion.

We first described autoimmunity complicating alemtuzumab (CAMPATH-1H)treatment in 1999 (Coles et al., 1999), and have continued to observethis complication of, what is increasingly recognized as, a highlyeffective therapy for early relapsing-remitting multiple sclerosis(Coles et al., J Neurology 253, 98-108 (2006); Coles et al., 1999 and2008). Our studies described below involved a series of cohorts ofavailable patients and were aimed at understanding this unprecedented“model” of human autoimmunity occurring in a subset of MS patientstreated by alemtuzumab.

The immune state is radically altered following exposure to alemtuzumab.T cells regenerating into the lymphopenic environment generated byalemtuzumab are highly proliferative and skewed towards auto-reactivity.However, these cells are highly unstable and short-lived. Whilst theirfate has not previously been directly addressed (King et al., Cell 117,265-277 (2004)), we show that these cells are dying rapidly byapoptosis. High and sustained levels of T cell apoptosis may explain whya single dose of alemtuzumab induces T cell lymphopenia lasting severalyears even though the half-life of circulating alemtuzumab is only sixdays and hematological precursors are not depleted (Gilleece et al.,Blood 82, 807-812 (1993)).

Against that background, we show that patients with secondaryautoimmunity have higher rates of T cell apoptosis, but no greater Tcell lymphopenia, than those without autoimmunity, suggesting increasedcell cycling in this group. These perturbations of T cell cycling areassociated with significantly higher serum IL-21 expression, which wehave found is genetically determined in at least some cases.Furthermore, susceptibility to lymphopenia-associated autoimmunity ismanifest before lymphocyte depletion, with pre-treatment IL-21 levelspredicting with accuracy (positive predictive value of more than 70%,e.g., 83%, and negative predictive value of more than 62%, e.g., 72%)the development of autoimmunity months to years after exposure toalemtuzumab. Without wishing to be bound by any theory, we believe thatby driving cycles of T cell expansion and death to excess, IL-21increases the stochastic opportunities for T cells to encounterself-antigen and break tolerance, hence promoting autoimmunity.

In summary, our findings provide the first exploration oflymphopenia-induced autoimmunity in man, and provide a conceptualframework for understanding lymphopenia-associated autoimmunity thatgoes beyond the narrow context of treating multiple sclerosis withalemtuzumab. The concept is that first therapeutic lymphocyte depletion,and secondly genetically restricted overproduction of IL-21, leads to astate of excess T cell cycling and reduced survival, which promotesautoimmunity in humans. These findings provide bases for the presentinvention.

This invention provides methods for managing MS patients whenconsidering lymphocyte depleting therapy such as alemtuzumab therapy.For example, our invention provides methods for identifying an MSpatient who has elevated IL-21 compared to the norm (i.e., levels ofIL-21 in control subject(s) as described below), and methods foridentifying an MS patient who is at increased risk of developingsecondary autoimmunity following lymphocyte depletion. These methodscomprise the step of measuring IL-21 (e.g., intracellular orextracellular protein levels, RNA transcript levels, or IL-21 activitylevels; see discussions below) in a blood sample from the patient, andcomparing the IL-21 value to the normal IL-21 value. Alternatively, inlieu of or in addition to the blood test, one can genotype the patientfor the presence or absence of one or more of SNP genotypes of A/A atSNP rs13151961, G/G at SNP rs6822844, and C/C at SNP rs6840978, wherethe presence of one, two or all three of these genotypes is associatedwith elevated IL-21. As discussed above, elevated IL-21 is associatedwith increased risk of developing secondary autoimmunity in the MSpatient following lymphocyte depletion, as compared to MS patients whodo not have elevated IL-21.

Identification of a patient by the methods of the invention may befollowed by a number of further steps contemplated by the invention. Forexample, the patient can be informed of the increased risk of developingsecondary autoimmunity following lymphocyte depleting therapy, or lackof such risk, based on his/her IL-21 level or genotype. Thus, theinvention will allow individualized counseling of the risks of thetherapy before commitment to the therapy. The health care provider canconsider therapeutic options in view of the risk of secondaryautoimmunity and provide a recommendation, including, for example,administering an IL-21 antagonist prior to, during, or after lymphocytedepleting therapy, or selecting a treatment regimen that does notinvolve lymphocyte depletion.

The health care provider also can consider risk management plans for apatient who elects to undergo lymphocyte depleting therapy. For example,the health care provider can inform the patient of a need for heightenedmonitoring for development of secondary autoimmunity after lymphocytedepleting therapy in view of his/her increased risk of developingsecondary autoimmunity. The health care provider also can recommend anappropriate monitoring regimen following lymphocyte depleting therapy.An appropriate monitoring regimen for patients at risk may include,without limitation, more frequent monitoring for secondary autoimmunityafter lymphocyte depleting therapy at an interval of, for example, oneweek, two weeks, one month, two months, three months, six months, or oneyear. The monitoring may need to be continued for an extended period oftime, for example, more than one year, two years, three years, fouryears, five years, or more, because some patients may not present withsecondary autoimmunity until well after one year following lymphocytedepletion therapy. Heightened monitoring also may entail, for example,more thorough medical examination (e.g., more blood tests) by aspecialist for any signs of secondary autoimmunity. Moreover,pharmacists or clinical staff who distribute a lymphocyte depleting drugto a patient for treating MS may be required to counsel the patient onthe increased risk of developing secondary autoimmunity following thedrug use, in the event that the patient has an elevated level of IL-21and/or has the particular IL-21 genotypes described herein that havebeen associated with elevated serum IL-21. The pharmacists or clinicalstaff may also be required to obtain informed consent from the patientprior to distributing the drug to the patient.

Multiple Sclerosis Patients

The methods and compositions of this invention can be used in thecontext of any form of MS, for example, relapsing-remitting MS, primaryprogressive MS, and secondary progressive MS. MS patients in the contextof this invention are those who have been diagnosed as having a form ofMS by, for example, the history of symptoms and neurological examinationwith the help of tests such as magnetic resonance imaging (MRI), spinaltaps, evoked potential tests, and laboratory analysis of blood samples.

Multiple sclerosis (“MS”), also known as disseminated sclerosis, is anautoimmune condition in which the immune system attacks the centralnervous system, leading to demyelination (Compston and Coles, 2008). MSdestroys a fatty layer called the myelin sheath that wraps around andelectrically insulates nerve fibers. Almost any neurological symptom canappear with the disease, and often progresses to physical and cognitivedisability (Compston and Coles, 2008). MS takes several forms. Newsymptoms can occur in discrete attacks (relapsing forms), or slowlyaccumulate over time (progressive forms) (Lublin et al., Neurology 46(4), 907-11 (1996)). Between attacks, symptoms may go away completely(remission), but permanent neurological problems often occur, especiallyas the disease advances (Lublin et al., 1996). Several subtypes, orpatterns of progression, have been described, and they are important forprognosis as well as therapeutic decisions. In 1996 the United StatesNational Multiple Sclerosis Society standardized four subtypedefinitions: relapsing-remitting, secondary progressive, primaryprogressive, and progressive relapsing (Lublin et al., 1996).

The relapsing-remitting subtype is characterized by unpredictable acuteattacks, called exacerbations or relapses, followed by periods of monthsto years of relative quiet (remission) with no new signs of diseaseactivity. This describes the initial course of most individuals with MS(Lublin et al., 1996).

Secondary progressive MS begins with a relapsing-remitting course, butsubsequently evolves into progressive neurologic decline between acuteattacks without any definite periods of remission, even thoughoccasional relapses and minor remissions may appear (Lublin et al.,1996).

The primary progressive subtype is characterized by a gradual but steadyprogression of disability with no obvious remission after their initialMS symptoms appear (Miller et al., Lancet Neurol 6 (10), 903-12 (2007)).It is characterized by progression of disability from onset, with no, oronly occasional and minor, remissions and improvements (Lublin et al.,1996). The age of onset for the primary progressive subtype is usuallylater than other subtypes (Miller et al., 2007)).

Progressive relapsing MS is characterized by a steady neurologicaldecline with acute attacks that may or may not be followed by somerecovery. This is the least common of all the subtypes describedhereinabove (Lublin et al., 1996).

Cases with non-standard behavior have also been described, sometimesreferred to as borderline forms of MS (Fontaine, Rev. Neurol. (Paris)157 (8-9 Pt 2): 929-34 (2001)). These forms include Devic's disease,Balo concentric sclerosis, Schilder's diffuse sclerosis, and Marburgmultiple sclerosis (Capello et al., Neurol. Sci. 25 Suppl 4: S361-3(2004); Hainfellner et al., J. Neurol. Neurosurg. Psychiatr. 55 (12):1194-6 (1992)).

Lymphocyte Depletion in Multiple Sclerosis Patients

As used herein, “lymphocyte depletion” is a type of immunosuppression byreduction of circulating lymphocytes, e.g., T cells and/or B cells,resulting in lymphopenia. Prolonged lymphocyte depletion is seen when,for example, autologous bone marrow transplantation (BMT) or totallymphoid irradiation is used to treat multiple sclerosis. See, e.g., Coxet al., Eur. J. Immunol. 35, 3332-3342 (2005). For example, lymphocytedepletion can be achieved by a combined use of thymoglobulin,cyclophosphamide and whole body irradiation. Lymphocyte depletion in MSpatients also can be achieved by a number of drug treatments. Forexample, a humanized anti-CD52 monoclonal antibody, CAMPATH-1H(alemtuzumab), has been used in lymphocyte depleting therapy to treat MSpatients. CAMPATH-1H-induced lymphopenia has been shown to effectivelyreduce central nervous system inflammation both clinically andradiologically (Coles et al., Ann. Neurol. 46, 296-304 (1999); Coles etal., 2008).

Other agents can also be used in lymphocyte depleting therapy to treatMS patients. These agents can be those that cause lymphocyte cell deathor inhibit lymphocyte functions. They include, without limitation, (1)agents targeting CD-52-bearing cells, such as agents biologicallysimilar to alemtuzumab, i.e., other anti-CD52 antibodies (e.g.,chimeric, humanized, or human antibodies) that bind to the same or adifferent epitope as alemtuzumab or compete with alemtuzumab for bindingto CD52, and soluble CD52 polypeptides that compete with cell surfaceCD52 for binding to ligand(s) of CD52; (2) biomolecules such aspeptides, proteins, and antibodies (e.g., chimeric, humanized, or humanantibodies) that target cell-surface molecules on lymphocytes, such asanti-CD4 antibodies, anti-CD20 antibodies (e.g., rituximab), anti-TCRantibodies, and anti-integrin antibodies (e.g., natalizumab); (3)cytotoxins (e.g., apoptosis-inducing agents, cyclophosamide, alkylatingagents, and DNA intercalators) delivered specifically or nonspecificallyto lymphocytes; and (4) antigen-binding portions of the aforementionedantibodies. The antibodies may include, without limitation, monoclonalantibodies, bifunctional antibodies, oligoclonal antibodies, andpolyclonal antibodies.

The term “antigen-binding portion” as used herein refers to one or morefragments of an antibody that retain the ability to specifically bind tothe same antigen as the whole antibody from which the portion isderived. Examples of “antigen-binding portion” include, withoutlimitation, a Fab fragment, a F(ab′)2 fragment, a Fd fragment, a Fvfragment, a dAb fragment, an isolated complementarity determining region(CDR), scFv, and a diabody. The antibodies and antigen-binding portionsthereof useful in this invention can be made by any methods well knownin the art. Any of the above lymphocyte depleting therapies can causelymphopenia, and in some patients, the lymphopenia leads to secondaryautoimmunity.

Secondary Autoimmunity in MS Patients

Autoimmunity is referred to herein as “secondary autoimmunity” when itarises subsequent to the onset of a first (“primary”) disease, forexample, a “primary” autoimmune disease. Secondary autoimmunitysometimes arises in MS patients having, or having had, lymphopeniafollowing, e.g., lymphocyte depleting therapy. In some individuals,secondary autoimmunity arises soon after lymphocyte depleting therapy(e.g., treatment with alemtuzumab). In other individuals, secondaryautoimmunity may not arise until months or years after lymphocytedepleting therapy; in some of those individuals, by the time theydevelop secondary immunity, substantial lymphocyte recovery (totallymphocyte count) may have occurred so that they may no longer belymphopenic.

Secondary autoimmunity arising in lymphopenic MS patients can be anytype of autoimmune condition other than MS, including but not limited tothyroid autoimmunity (e.g., Graves' disease), immune thrombocytopenia(ITP), Goodpasture's disease, autoimmune neutropenia, autoimmunehemolytic anemia, and autoimmune lymphopenia. Techniques for diagnosingand monitoring these autoimmune diseases are well known to those skilledin the art, including assessment of symptoms and medical examinationsuch as blood analysis. The invention contemplates the use of any knownmethods. For example, autoantibody levels in a patient's body fluid(e.g., blood) can be determined as a means of detecting signs ofautoimmunity. Specifically, anti-nuclear antibodies, anti-smooth muscleantibodies, and anti-mitochrondrial antibodies can be measured. In theevent anti-nuclear antibodies are detected, additional assays can beperformed to measure anti-double-stranded DNA antibodies,anti-ribonucleoprotein antibodies, and anti-La antibodies. Anti-thyroidperoxidase (TPO) and anti-thyroid stimulating hormone (TSH) receptorantibodies can be measured to detect autoimmune thyroid diseases; ifanti-TPO or anti-TSH receptor antibodies are detected, one can measurewhether thyroid function is affected by measuring free T3, free T4 andTSH levels. Anti-platelet antibodies can be measured to detectautoimmune thrombocytopenia; and a measurement of blood platelet levelsmay serve to determine if the presence of anti-platelet antibodies iscausing a reduction in platelet number.

Measurement of IL-21

In the methods of this invention, IL-21 can be measured by a number oftechniques. IL-21 is a member of the gamma-c-related cytokine family,and has potent activity in promoting T and B cell proliferation andnatural killer (NK) cell cytotoxicity. IL-21 is mainly expressed byactivated CD4+ T cells (e.g., Th17 cells) and is important in T helpertype I (Th1) immune responses (Weiss et al., Expert Opin Biol. Ther. 7,1705-1721 (2007); Sivakumar et al., Immunology 112, 177-182 (2004)). Thehuman IL-21 gene encodes a polypeptide precursor of 162 amino acidresidues and a fully processed mature protein of 133 amino acid residues(about 15 kD); the gene is located on human chromosome 4q26-27(Sivakumar et al., 2004). The receptor for IL-21 (IL-21R) has been foundon resting peripheral B cells, activated peripheral blood mononuclearcells, and in germinal center of human lymph nodes (Marleau et al., J.Leukocyte Biol. 78, 575-584 (2005)).

Methods of measuring IL-21 are well known to those skilled in the art.According to some embodiments of the present invention, a body fluidsample (e.g., blood, serum, plasma, urine, saliva, or cerebrospinalfluid) is obtained from a patient, and the IL-21 level in the sample ismeasured, by any assay suitable for protein detection, including but notlimited to, immunoassays such as enzyme-linked immunosorbent assays(ELISA). Commercial ELISA kits for measuring human IL-21 are availablefrom, for example, KOMABIOTECH (Seoul, Korea), Bender MedSystems(Burlingame, Calif.), and eBioscience (San Diego, Calif.).

Alternatively, IL-21 transcript levels in IL-21 producing cells (e.g.,Th17 cells) obtained from the patient can be measured by Northern blotanalysis and quantitative polymerase chain reaction (Q-PCR). Methods ofisolating Th17 cells are well known in the art, and isolation can bedone by using commercially available kits, e.g., kits from MiltenyiBiotec (Auburn, Calif.), eBioscience (San Diego, Calif.). In someembodiments, IL-21 levels are measured by cytokine staining and flowcytometry in which an anti-IL-21 antibody linked to a detectable moietyis used to detect the intracellular level of IL-21 in IL-21 producingcells from the patient. IL-21 also can be measured in terms of activityin a biological assay, e.g., by measuring proliferative responses of Tcells to a combination of IL-21 and IL-15 using, e.g., CFSE(carboxyfluorescein succinimidyl ester) (Zeng et al., Curr. Protoc.Immunol. 78:6.30.1-6.30.8 (2007)). Another method of measuring IL-21 isbased on IL-21-induced tyrosine phosphorylation of Stat3 in splenicCD8(+) T cells using a flow cytometry-based analysis (Zeng et al.,2007). Those of skill in the art will readily appreciate other suitablemeans for measuring IL-21.

In the methods of this invention, the reference (or index) value fordetermining whether a patient has elevated (abnormally high) IL-21 isthe value of IL-21 of a control subject, or the mean value of IL-21 of agroup of control subjects, obtained using the same assay that isconducted at the same or a different time. The control subject is anormal or healthy subject, who, in this context, is an individualwithout any ongoing known inflammatory condition, including without anautoimmune disease (without any detectable symptoms of an autoimmunedisease). In some embodiments, the control subjects are not lymphopenic.An increase of IL-21 level by about 10%, 20%, 30%, 40%, 50%, 100%,two-fold, three-fold, four-fold, five-fold, ten-fold, twenty-fold,thirty-fold, forty-fold, fifty-fold, one hundred-fold or more may beconsidered a significant increase. Certain statistical analyses can beapplied to determine if the IL-21 level in a test sample issignificantly different from the control level. Such statisticalanalyses are well known to those skilled in the art and may include,without limitation, parametric (e.g., two-tailed Student's t-test) ornon-parametric (e.g., Wilcoxon-Mann-Whitney U test) tests.

Detecting IL-21 SNP Genotypes

In some methods of this invention, genotyping is used to predict whethera patient is prone to having (i.e., at risk of having or likely to have)elevated IL-21 and hence at risk of developing secondary autoimmunitywhile having lymphopenia. “Genotyping” refers to the process ofdetermining the genotype of an individual by the use of biologicalassays. Methods of genotyping are well known to those skilled in theart, and include, without limitation, PCR, DNA sequencing,allele-specific oligo (ASO) probes, and hybridization to DNA microarraysor beads. Genotyping can be partial, i.e., only a small fraction of anindividual's genotype is determined. In the context of this invention,only certain SNPs need to be detected. A SNP is a DNA sequence variationoccurring when a single nucleotide—A, T, C, or G—in a correspondingportion of the genome differs between members of a species or betweenpaired chromosomes in an individual. Known human SNPs are assignedreference SNP (refSNP or rs) identification numbers in the public-domainarchive Single Nucleotide Polymorphism Database (dbSNP) hosted at theNational Center for Biotechnology Information (NCBI).

The present inventors have discovered that the minor SNP genotypes ofrs13151961 A/A, rs6822844 G/G and rs6840978 C/C are associated withsignificantly higher levels of serum IL-21 compared to individuals whodo not have these genotypes. MS patients having one or more of these SNPphenotypes, thus, have an increased susceptibility to developingsecondary autoimmunity after lymphocyte depletion, compared to MSpatients who do not have these genotypes.

Timing of Obtaining IL-21 Information

Obtaining information on IL-21 (IL-21 levels or IL-21-related SNPgenotypes) of an MS patient is useful in selecting treatment andpost-treatment monitoring regimens for the patient. When the informationis obtained prior to MS therapy, the patient can be informed of therelative risk of developing secondary autoimmunity following lymphocytedepleting therapy and treatment decisions can be made accordingly. Thepatient also can be informed of a need for heightened post-treatmentmonitoring, e.g., more frequent and more thorough examination by aspecialist, if he is classified as “at risk.” Thus, the IL-21information improves risk management (by physicians, pharmacists, andpatients) in MS treatment.

Obtaining IL-21 information during or after MS treatment also will behelpful in monitoring secondary autoimmunity development and treatment.As noted above and further described below, we have discovered thatfollowing lymphocyte depleting therapy, MS patients who go on to developsecondary autoimmunity have a much larger increase in their serum IL-21,as compared to MS patients who do not develop secondary autoimmunity.The latter group of MS patients produce only slightly more IL-21following lymphocyte depletion. Thus, by measuring IL-21 productionafter lymphocyte depleting treatment, one also can predict the risk ofsecondary autoimmunity, which may not occur until months or years afterthe treatment.

Treating Secondary Autoimmunity

A secondary autoimmunity disease arising in MS patients can be treatedbased on the type of the disease. In some embodiments of the presentinvention, the secondary autoimmunity can be treated by using aneffective dose of an IL-21 antagonist. An IL-21 antagonist can be atherapeutic agent that inhibits IL-21 activity, e.g., an agent thatinhibits the interaction between IL-21 and IL-21R. “An effective dose”refers to the amount of an inhibiting agent sufficient to inhibit IL-21activity in a patient such that symptoms of the secondary autoimmunedisease are alleviated or prevented. IL-21 antagonists can be, forexample, chimeric, humanized, or human monoclonal antibodies to humanIL-21 or IL-21R, or soluble IL-21R proteins. See also, e.g., U.S. Pat.No. 7,410,780 and U.S. Patent Application Publication No. 20080241098,the entire teachings of which are incorporated herein by reference.Pharmaceutical compositions containing an IL-21 antagonist can be madeaccording to methods known to those in the art. Pharmaceuticalcompositions containing IL-21 antagonists can be administered to apatient using a suitable method known in the art, e.g., intravenously,intramuscularly, or subcutaneously.

Kits for Treating and Testing MS Patients

The present invention provides kits for treating multiple sclerosis. Akit of this invention can contain, inter alia, a lymphocyte depletingdrug (e.g., alemtuzumab), and a written instruction for informing apatient or a healthy care provider of contraindications of the drug, forexample, the potential for an increased risk of developing a secondaryautoimmune disease following treatment with the drug. The increased riskcan be associated with or indicated by (i) elevated IL-21, or (ii) thepresence of one or more genotypes of single-nucleotide polymorphisms(SNPs) selected from the group consisting of: A/A at SNP rs13151961, G/Gat SNP rs6822844, and C/C at SNP rs6840978.

In other embodiments, the invention provides kits for detecting serumIL-21 in an MS patient, and/or for identifying MS patients at increasedrisk of developing a secondary autoimmune disease following lymphocytedepletion. Such kits can comprise an anti-IL-21 antibody, or anantigen-binding portion thereof, or a soluble IL-21 receptor, andoptionally an instruction directing a user to take a blood sample from apatient, and optionally one or more reagents for detecting the bindingof the antibody, portion, or soluble IL-21 receptor to IL-21 in theblood sample from the MS patient. Such kits will have been validated orapproved by an appropriate regulatory authority for making medicaldiagnosis in patients, such as MS patients.

In still other embodiments, the invention provides kits for identifyingan MS patient who is at increased risk of developing a secondaryautoimmune disease following lymphocyte depletion. The kits can compriseone or more reagents suitable for identifying the presence or absence ofone or more SNP genotypes selected from the group consisting of: SNPrs13151961, SNP rs6822844, and SNP rs6840978, in a sample obtained froman MS patient, and an instruction directing a user to take a sample froman MS patient.

Assessing T Cell Responsiveness to MS Treatment

This invention provides methods for assessing T cell responsiveness totreatment with lymphocyte depleting therapy in an MS patient. Themethods entail measuring caspase-3 in T cells obtained from the patientafter the treatment. An increase in caspase-3 (e.g., caspase-3 protein,RNA transcript, and/or activity levels) in the T cells compared to Tcells from an MS patient not receiving the treatment indicates that theT cells in the treated patient have responded to the treatment. Thesemethods are based on our discovery that T cells from people withuntreated MS are apoptosis-resistant, and that this resistance isassociated with under-expression of caspase-3. But after lymphocytedepleting therapy, caspase-3 expression is significantly increased in Tcells, reaching levels seen in healthy people.

Techniques of measuring caspase-3 in T cells are well known in the art.For example, one can obtain cell extracts from T cells using techniqueswell known in the art, and measure caspase-3 protein levels by, e.g.,ELISA. Commercial ELISA kits for measuring human caspase-3 are availablefrom, e.g., Bender MedSystems (Burlingame, Calif.), EMD Chemicals, Inc.(San Diego, Calif.), and R&D Systems, Inc. (Minneapolis, Minn.).Alternatively, caspase-3 transcript levels can be measured in T cellsby, for example, Northern blot analysis or quantitative PCR. Caspase-3can also be measured in terms of activity in a biological assay, e.g.,by measuring its protease activity. Commercial kits for measuringcaspase-3 activity are available from, e.g., Roche Applied Science(Indianapolis, Ind.), and Invitrogen (Carlsbad, Calif.).

Unless otherwise defined, all technical and scientific terms used hereinhave the same meaning as commonly understood by one of ordinary skill inthe art to which this invention belongs. Exemplary methods and materialsare described below, although methods and materials similar orequivalent to those described herein can also be used in the practice ortesting of the present invention. All publications and other referencesmentioned herein are incorporated by reference in their entirety. Incase of conflict, the present specification, including definitions, willcontrol. Although a number of documents are cited herein, this citationdoes not constitute an admission that any of these documents forms partof the common general knowledge in the art. Throughout thisspecification and embodiments, the word “comprise,” or variations suchas “comprises” or “comprising” will be understood to imply the inclusionof a stated integer or group of integers but not the exclusion of anyother integer or group of integers. The materials, methods, and examplesare illustrative only and not intended to be limiting.

The following examples are meant to illustrate the methods and materialsof the present invention. Suitable modifications and adaptations of thedescribed conditions and parameters normally encountered in the artwhich are obvious to those skilled in the art are within the spirit andscope of the present invention.

EXAMPLES

In the following examples, all patients had relapsing-remitting multiplesclerosis and were participants in one of two clinical trials: CAMMS-223and CAMMS-224 (REC 02/315 and 03/078) in which alemtuzumab was given byintravenous infusion of 12-24 mg/day for five days, followed byre-treatment at 12 months. Patients and controls consented tovenesection for research purposes (LREC 02/263) and all were free fromexposure to other disease modifying agents, including steroids, for atleast one month at the time of blood sampling.

Lymphocyte proliferation and apoptosis data were generated by across-sectional study of fresh, ex vivo cells from 65 patients and 21healthy controls (7 males, mean age 34 years). This generated hypothesesabout T-cell cycling in the pathogenesis of secondary autoimmunity,which were tested on samples available at nine months after alemtuzumabtreatment, which was chosen as the earliest time point in which T cellapoptosis could be robustly analyzed. Of the 29 samples available atthis time point, 10 met our study definition of autoimmunity (1 male,mean age 36 years) compared to 10 without autoimmunity (3 male, mean age38 years). Autoimmunity was defined as development of a novel autoimmunedisease (with or without autoantibodies), or persistent significanttiters of autoantibodies (present on at least two occasions at leastthree months apart) without clinical disease. “No autoimmunity” wasdefined as the absence of an autoimmune disease and autoantibodies forat least 18 months post-alemtuzumab in this study. Of the ten patientswith autoimmunity, three had autoantibodies only (antinuclearantibodies). Next, serum IL-21 was measured serially in: 15 randomlyselected patients with autoimmunity—five of whom had been studied asabove (three males, mean age 34 years; twelve with thyroid autoimmunity,one with Goodpasture's disease, one with ITP, and one with antinuclearantibodies only), and fifteen randomly selected patients withoutautoimmunity—six of whom had been studied as above, (five males, meanage 31 years) and nineteen healthy controls (seven male, mean age 33years).

73 subjects were studied for genetic analysis. Of these, 23 met thedefinition of “no autoimmunity” and 27 had secondary autoimmunity afteralemtuzumab (six with autoantibodies only: four with antinuclear and twowith anti-smooth muscle antibodies; eighteen with thyroid autoimmunity,two with ITP and one with Goodpasture's disease). The 23 remainingsubjects could not be categorised on the basis of transient autoantibodyproduction and/or insufficient time since treatment with alemtuzumab.

For all the statistical analysis described in the following examples,data were analyzed using SPSS 12.0.1 for Windows. Following assessmentfor normality, parametric (Student's t-test) or non-parametric(Wilcoxon-Mann-Whitney) tests were performed. P values are statedthroughout the text, where a value of p<0.05 was considered asstatistically significant, modified by a Bonferroni correction whereindicated.

Example 1 Alemtuzumab Induces a T Cell Lymphopenia

A single dose of alemtuzumab resulted in the depletion of CD4+ and CD8+Tlymphocytes to 5.6% and 6.8% respectively of baseline values at month 1,and 30.3% and 40.8% respectively at month 12 (data not shown).

Example 2 T Cells from Patients with Untreated Multiple Sclerosis areResistant to Cell Death

For various assays performed in this Example, different cross-sectionaland longitudinal samples were used according to availability. As aprelude to measuring lymphocyte cell cycling after alemtuzumab, weexamined the proliferative response of T cells, unstimulated or inculture with myelin basic protein (MBP) or the thyroid-stimulatinghormone receptor (TSHr), between untreated patients with multiplesclerosis and normal controls (FIGS. 1A and 1B).

A. Peripheral Mononuclear Cell Cultures

Peripheral blood mononuclear cells (PBMCs) were isolated fromheparinized blood by centrifugation on a Ficoll-Paque density gradient(Amersham Pharmacia Biotech). Whole PBMCs were immediately suspended inculture medium (RPMI) containing 1% penicillin, 1% streptomycin and 10%fetal calf serum (Sigma 55394) and adjusted to a concentration of 10⁶/mLviable cells (determined by trypan blue exclusion). To induce passivecell death, PBMCs were incubated for 72 hours in media alone withoutadditional growth factors. Fas-mediated apoptosis was induced byculturing PBMCs for 48 hours with soluble anti-CD28 (1 μg/mL: kindlydonated by M. Frewin, University of Oxford) in anti-CD3 mAb-precoatedplates (1 μg/mL—BD Pharmingen), followed by 18 hours incubation withactivating anti-human Fas (clone CH11, 1 μg/mL—Upstate Biotechnology,Lake Placid, N.Y.).

B. Detection of Apoptosis

Apoptotic T cells were detected by staining cells with:allophycocyanin-conjugated mouse anti-human monoclonal antibodiesagainst CD3 (Serotec MCA463APC), CD4 (Serotec MCA1267APC) and CD8(Serotec MCA1226APC), FITC-conjugated annexin-V and Propidium Iodide (BDPharmingen). Fluorescence was detected by flow cytometry (FACSCALIBUR:Becton Dickinson, Mountain View, Calif.). Based on forward and sidescatter, a wide lymphocyte gate was drawn to include live and apoptoticlymphocytes (having reduced FSc and increased SSc). At least 15,000events within the gate were collected and analyzed using WinMDI 2.8software. Early apoptotic cells were defined as annexinV⁺PI⁻, and lateapoptotic or necrotic cells as annexinV⁺PI⁺ (Aubry et al., Cytometry 37,197-204 (1999)). Apoptotic cell death was defined as total cell death(annexinV⁺PI⁻ plus annexinV⁺PI⁺) blocked by pan-caspase inhibition withQ-VD-OPh (RnD Systems OPH001).

C. Proliferation Assays

PBMCs were loaded with the cell division tracking dye CFSE(carboxyfluorescein diacetate succinimidyl ester) (Lyons et al. MethodsCell Biol. 63, 375-398 (2001)) and cultured with 50 μg/mL myelin basicprotein (MBP: RDI-TRK8M79/LYO) or 1 μg/mL thyroid stimulating hormonereceptor extracellular domain bound to a matrix binding protein (TSHr:kindly donated by M. Ludgate, Cardiff University). After 10 days CFSEstaining in cells, identified by specific surface markers (CD4, CD8),was analysed by flow cytometry. Precursor frequency (defined as theproportion of lymphocytes that left the parent population to undergo atleast two cell divisions) and proliferation index (defined as the sum ofthe cells in all generations divided by the computed number of parentcells) were calculated using Modfit LT 3.0 (Verity Software). Absolutenumber of surviving cells was measured by comparison with a fixed numberof inert beads (BD CALIBRITE, BD Biosciences), included in cultures.

D. Results

There was no difference in the proliferative response of T cells,unstimulated or in culture with myelin basic protein (MBP) or thethyroid stimulating hormone receptor (TSHr), between untreated patientswith multiple sclerosis and normal controls (FIGS. 1A and 1B).Conversely, survival of T cells from untreated patients with multiplesclerosis was ≧4 fold greater than that of controls (p<0.005; FIG. 1C),suggesting that reduced T cell death is a feature of untreated multiplesclerosis. We confirmed this by demonstrating that T cells fromuntreated patients are resistant both to passive and Fas-mediatedapoptosis compared with healthy controls (passive: 0.3% v. 6.7%,p=0.0016; and Fas-mediated: 2.9% v. 15.5%, p=0.0018; FIGS. 1E and 1F).Example 3: T cells that regenerate after alemtuzumab are highlyproliferative, skewed towards self reactivity and susceptible toapoptosis

Using the assays described in Example 2, we found that followingalemtuzumab, the proportion of T cells responding to self-antigens(precursor frequency) and the degree of proliferation (proliferativeindex) were significantly increased compared to untreated patients andhealthy controls. For example at month 3, unstimulated T cellproliferation was >6.5 fold that of untreated patients and proliferationin response to MBP and TSHr stimulation was increased by 900% and 700%respectively (all p<0.01: FIGS. 1A and 1B). T cell apoptosis was alsosignificantly increased post-alemtuzumab. In response to antigenicstimulation, the proportion of T cells undergoing apoptosis at sixmonths was 10 fold greater than at baseline (FIG. 1D; p<0.001 for allantigens) resulting in fewer viable T cells at the end of culture (FIG.1C). Passive and Fas-mediated apoptosis were also increased afteralemtuzumab, with rates at least double those observed in the healthycontrol group (passive: 24.5%, 22.2% and 17.9% at 6, 9 and 12 months,respectively, compared to 6.7% in controls, all p<0.001; Fas-mediated37.8%, 35.8% and 29.9% at 6, 9 and 12 months, respectively, compared to15.5% in controls, all p<0.01; FIGS. 1E and 1F). Increased lymphocyteapoptosis after alemtuzumab was seen in both the CD4+ and CD8+subpopulations (FIGS. 1G and 1H) and persisted for at least 18 monthsafter alemtuzumab treatment (data not shown).

Example 4 T Cells from Untreated Patients with Multiple SclerosisUnder-Express Caspase 3

A. mRNA Analysis

PBMCs, immediately ex-vivo or after culture with MBP or polyclonalstimulation, were positively separated, using 20 μL of magnetic beads(Miltenyi Biotec; CD19 Microbeads, CD3 Microbeads, CD14 Microbeads) per1×10⁷ cells loaded into a MACS® LS Column. Magnetically retained cellswere eluted, washed and stored in RNAlater™ at −70° C. (cell purityconsistently 95-98%, data not shown).

Fas, FasL, Bcl-2, Bcl-X1, Bad, Bax, Bid, Bim, Survivin, c-FLIP, andCaspase 3, 8 and 9 expression was determined by semi-quantitativeRT-PCR. mRNA was extracted from cells stored in RNAlater™ using theRNEASY Mini Kit (QIAgen) and reverse transcribed to cDNA using thePRO-STAR First Strand RT-PCR Kit (Stratagene). PCR primers and probeswere designed using PRIMER EXPRESS (PE Biosystems, Foster City, Calif.,USA), and purchased from Oswel DNA service. mRNA sequence informationwas obtained from GenBank. Quantitative real-time PCR was performed onan ABI Prism 7900HT Sequence Detection System (Perkin Elmer) using PCRMastermix containing ROX (Eurogentec RT-QP2X-03). Primer and probesequences were: Bc1-2 For: 5′-CCT GTG GAT GAC TGA GTA CCT GAA-3′ (SEQ IDNO:1), Rev 5′-CAC CTA CCC AGC CTC CGT TA-3′ (SEQ ID NO:2), JOE-labelledprobe 5′-CGG CAC CTG CAC ACC TGG ATC-3′ (SEQ ID NO:3); Bcl-Xl For 5′-TTCAGT CGG AAA TGA CCA GAC A-3′ (SEQ ID NO:4), Rev 5′-GAG GAT GTG GTG GAGCAG AGA-3′ (SEQ ID NO:5), FAM-labelled probe 5′-TGA CCA TCC ACT CTA CCCTCC CAC CC-3′ (SEQ ID NO:6); Fas For 5′-AAA AGC ATT TTG AGC AGG AGA GTATT-3′ (SEQ ID NO:7), Rev 5′-GGC CAT TAA GAT GAG CAC CAA-3′ (SEQ IDNO:8), JOE-labelled probe 5′-CTA GAG CTC TGC CAC CTC TCC ATT-3′ (SEQ IDNO:9); FasL For 5′-AAG AAA GTG GCC CAT TTA ACA G-3′ (SEQ ID NO:10), Rev5′-AGA AAG CAG GAC AAT TCC ATA GGT-3′ (SEQ ID NO:11), FAM-labelled probe5′-CAA CTC AAG GTC CAT GCC TCT GG-3′ (SEQ ID NO:12); Survivin For 5′-CTGCCT GGC AGC CCT TT-3′ (SEQ ID NO:13), Rev 5′-CTC CAA GAA GGG CCA GTTCTT-3′ (SEQ ID NO:14), FAM-labelled probe 5′-TCA AGG ACC ACC GCA TCT CTACAT T-3′ (SEQ ID NO:15); c-FLIP For 5′-GTG GAG ACC CAC CTG CTC-3′ (SEQID NO:16), Rev 5′-GGA CAC ATC AGA TTT ATC CAA ATC C-3′ (SEQ ID NO:17),FAM-labelled probe 5′-CTG CCA TCA GCA CTC TAT AGT CCG AAA CAA-3′ (SEQ IDNO:18); Caspase 8 For 5′-AGG AGG AGA TGG AAA GGG AAC TT-3′ (SEQ IDNO:19), Rev 5′-ACC TCA ATT CTG ATC TGC TCA CTT CT-3′ (SEQ ID NO:20),JOE-labeled probe 5′-CTC CCT ACA GGG TCA TGC TCT ATC AGA TTT CAG-3′ (SEQID NO:21); Caspase 3 For 5′-AAG ATC ATA CAT GGA AGC GAA TCA-3′ (SEQ IDNO:22), Rev 5′-CGA GAT GTC ATT CCA GTG CTT TTA-3′ (SEQ ID NO:23),FAM-labeled probe 5′-CTG GAA TAT CCC TGG ACA ACA GTT ATA AA-3′ (SEQ IDNO:24); Caspase 9 For 5′-TGC GAA CTA ACA GGC AAG CA-3′ (SEQ ID NO:25),Rev 5′-GAA CCT CTG GTT TGC GAA TCT C-3′ (SEQ ID NO:26), FAM-labeledprobe 5′-CAA AGT TGT CGA AGC CAA CCC TAG AAA ACC TTA-3′ (SEQ ID NO:27);Bad For 5′-CAG TGA CCT TCG CTC CAC ATC-3′ (SEQ ID NO:28), Rev 5′-ACG GATCCT CTT TTT GCA TAG-3′ (SEQ ID NO:29), JOE-labeled probe 5′-ACT CCA CCCGTT CCC ACT GCC C-3′ (SEQ ID NO:30); Bax For 5′-TTT CTG ACG GCA ACT TCAACT-3′ (SEQ ID NO:31), Rev 5′-GGT GCA CAG GGC CTT GAG-3′ (SEQ ID NO:32),JOE-labeled probe 5′-TGT CGC CCT TTT CTA CTT TGC CAG CA-3′ (SEQ IDNO:33); Bid For 5′-GCT GTA TAG CTG CTT CCA GTG TAG-3′ (SEQ ID NO:34),Rev 5′-GCT ATC TTC CAG CCT GTC TTC TCT-3′ (SEQ ID NO:35), JOE-labeledprobe 5′-AGC CCT GGC ATG TCA ACA GCG TTC-3′ (SEQ ID NO:36) and Bim For5′-ACC ACA AGG ATT TCT CAT GAT ACC-3′ (SEQ ID NO:37), Rev 5′-CCA TAT GACAAA ATG CTC AAG GAA-3′ (SEQ ID NO:38), FAM-labeled probe 5′-TAG CCA CAGCCA CCT CTC TCC CT-3′ (SEQ ID NO:39).

B. Results

T cell mRNA expression of caspase 3, the effector caspase common to bothapoptotic pathways, from untreated multiple sclerosis patients wasreduced compared to controls; this was significant for unstimulated andMBP-stimulated PBMCs (by 78% and 87% respectively, both p<0.05, aftercorrection for multiple comparisons), but not for polyclonal stimulatedcultures (FIG. 2A). A similar trend was seen in CD14+ cells (but notCD19+ cells) although this difference did not survive correction formultiple comparisons (FIG. 2B). After alemtuzumab, caspase 3 expressionwas significantly increased in T cells and monocytes, reaching levelsseen in healthy controls (p<0.05; FIGS. 2A and 2B). Expression of allother genes tested (listed in methods) was unchanged after alemtuzumab.

Thus, our studies show that T cells from people with untreated multiplesclerosis are resistant to apoptosis, and this resistance is associatedwith under-expression of caspase 3. Consistent with the position of thiseffector caspase at the convergence point of the extrinsic and intrinsicapoptotic pathways, we have demonstrated T cell resistance both toFas-mediated and passive apoptosis in our patients. Under-expression ofcaspase 3 has been described in some autoimmune diseases, including TypeI diabetes (Vendrame et al., Eur J Endocrinol 152, 119-125 (2005)),Hashimoto's thyroiditis and autoimmune polyendocrine syndrome-2(Vendrame et al., J Clin Endocrinol Metabjc (2006)). This is, however, anovel finding in multiple sclerosis.

Example 5 Secondary Autoimmunity after Alemtuzumab is Associated withExcessive T Cell Apoptosis

Having demonstrated increased lymphocyte proliferation and apoptosis asa generic response to treatment, we tested the relationship between Tcell apoptosis and development of autoimmunity after alemtuzumab,defined as development of a novel autoimmune disease and/or persistentautoantibodies above the normal range, after alemtuzumab, sustained overat least 3 months. Using this definition, T cells derived from patientswith autoimmunity (n=10) showed significantly higher levels of apoptoticcell death in all culture conditions at 9 months post-treatment, whencompared to T cells from non-autoimmune patients (n=10) studied at thesame time point (unstimulated 4.7% vs. 14.4%, Fas-mediated 18.2% vs.32.1%, MBP 7.6% vs. 17.6%, and TSHr 9.5% vs. 25.5%, p<0.01 for allcomparisons; FIG. 3). If a stricter definition of autoimmunity wasapplied, that being development of an autoimmune disease, excludingnonpathogenic antibody production, the difference remained, despitereducing the number in the autoimmune group to 7 (unstimulated, 4.7% vs.15.4%; Fas mediated, 18.2% vs. 31.7%; MBP, 7.6% vs. 20.2%; TSHr, 9.5%vs. 13.4%; P<0.02 for all comparisons).

There was no difference in the rate of T cell reconstitution between thetwo groups (e.g., at 6 months, CD4 counts are 0.15×10⁹/L vs. 0.19×10⁹/L;and CD8 counts 0.11×10⁹/L vs. 0.11×10⁹/L in those with and withoutautoimmunity, respectively), suggesting increased T cell cycling in theautoimmune group (data not shown).

Example 6 IL-21 Induces T Cell Proliferation and Apoptosis

A. IL-21 Assays and Spiking

Serum IL-21 was measured using the EBIOSCIENCE kit (88-7216-86) as perinstructions. Plates were read using a microplate reader (model 680,BioRad) at 450 nm. Unstimulated and polyclonally stimulated (1 μg/mLplate-bound anti-CD3 and 1 μg/mL soluble anti-CD28) PBMCs were spikedwith 5 pg/mL and 20 pg/mL rhIL-21 (EBIOSCIENCE 14-8219). CD4+ and CD8+apoptosis and proliferation were assessed as described above.

B. Results

We tested the effect of exogenous IL-21 on apoptosis and proliferationof human T cells in vitro. Spiking PBMCs from healthy controls withrhIL-21 led to an increase in the apoptotic death of unstimulated andpolyclonally stimulated CD4+ (FIG. 4A) and CD8+ (FIG. 4B) T cells in adose dependent manner (p<0.05 for all conditions). Spiking unstimulatedcells with rhIL-21 led to a small but significant increase in theproliferation of both CD4+ and CD8+ T cells; with an increase both inproliferative index (CD4+ and CD8+: 1.07 vs. 1.25, p=0.017; and 1.09 vs.1.32, p=0.017 respectively; FIG. 5A) and precursor frequency (CD4+ 0.007vs. 0.014, p=0.016; CD8+ 0.007 vs. 0.015, p=0.026; FIG. 5C). IL-21 didnot affect the proportion of CD4+ or CD8+ T cells proliferating inresponse to polyclonal stimulation (FIG. 5D), suggesting that they werealready maximally stimulated. IL-21, however, did lead to a significantincrease in the extent of CD8+ cell proliferation (proliferative index11.59 vs. 19.39, p=0.012; FIG. 5B).

Example 7 IL-21 Predicts the Development of Secondary Autoimmunity afterAlemtuzumab

At all time points in Example 6, the concentration of serum IL-21 wassignificantly greater in patients who developed secondary autoimmunitycompared to the non-autoimmune group (for all comparisons p<0.05; FIG.6A). We examined all pre-treatment serum samples from 84 patients whosubsequently went on to have alemtuzumab. After at least two years offollow up with these patients, we categorized them as being in the“autoimmune” group (n=35:32 patients with thyroid diseases, one ITP, oneGoodpasture's, and one Alopecia) or “non-autoimmune” group (n=49:patients with no or only transient (unsustained over six months)autoantibodies)). These pre-treatment sera had a statistically greatermean concentration of IL-21 than controls; however, this was entirelyaccounted for by high IL-21 levels in those patients who went on todevelop secondary autoimmunity. There was a highly significantdifference in mean pre-treatment IL-21 levels between those that went onto develop autoimmunity (464 pg/ml) and those that did not (229 pg/ml;p=0.0002) (FIG. 6B).

The association between induced-lymphopenia and autoimmunity has beenobserved in animal models. Under lymphopenic conditions, the remaining Tcells undergo extensive compensatory expansion in order to reconstitutethe immune system. This process, termed homeostatic proliferation,relies on stimulation through the TCR-self-peptide-MHC complex (Ge etal., P.N.A.S. 101, 3041-3046 (2004); Ge et al., P.N.A.S. 98, 1728-1733(2001); Kassiotis et al., J Exp. Med. 197, 1007-1016 (2003)) and resultsin a population skewed towards increased recognition of self-antigen, asseen in our studies. In addition, rapidly expanding T cells acquire thephenotype and functional characteristics of memory cells including:reduced dependence on co-stimulation, the ability to respond to lowerdoses of antigen than naïve cells, and the rapid secretion ofinflammatory cytokines on restimulation, so further promoting thebreakdown of self tolerance (Cho et al., JExp. Med. 192, 549-556 (2000);Goldrath et al. JExp. Med. 192, 557-564 (2000); Murali-Krishna et al., JImmunol 165, 1733-1737 (2000); Wu et al., Nat Med. 10, 87-92 (2004)).Yet, despite these changes, autoimmunity is not an inevitableconsequence of lymphopenia. Indeed, as with our patients, mostlymphopenic subjects did not develop autoimmunity, suggesting thatadditional “co-factors” are required.

We have demonstrated here for the first time in man that overproductionof IL-21 is the “second hit” required in the development of secondaryautoimmunity following otherwise successful treatment of multiplesclerosis with a lymphocyte depleting agent such as alemtuzumab. Ourstudies show that autoimmunity arises in lymphocyte-depleted patients,with greater T cell apoptosis and cell cycling driven by geneticallyinfluenced higher levels of IL-21 that are detectable even beforetreatment. Even before treatment, patients who went on to developsecondary autoimmunity had more than 2-fold greater levels of serumIL-21 than the nonautoimmune group, suggesting that serum IL-21 mayserve as a biomarker for the risk of developing autoimmunity months toyears after alemtuzumab treatment. Without wishing to be bound by anytheory, we believe that, by driving cycles of T cell expansion and deathto excess, IL-21 increases the probability of generating self-reactive Tcells, and hence, for autoimmunity. Thus, cytokine-induced abnormal Tcell cycling is a general principle of lymphopenia-associatedautoimmunity.

Example 8 IL-21 Genotype Influences IL-21 Expression and Associates withAutoimmunity

A. IL-21 Genotyping

In total, four SNPs, rs13151961, rs6822844, rs4833837 and rs6840978,which lie in a region of strong linkage disequilibrium containing fourgenes, KIAA1109-ADAD1-IL2-IL21, on chromosome 4q27 were tested. All fourSNPs were available as Applied Biosystems Assay-On-Demand (AoD)products. SNP genotyping was performed using Applied Biosystems TaqManmethodology according to the manufacturer's recommended conditions.Polymerase chain reaction (PCR) was performed on Applied Biosystems384-well 9700 Viper PCR machines, after which genotypes were called on a7900 High Throughput Sequence Detection System (SDS) using SDS SoftwareVersion 2.1. Each individual was genotyped in duplicate. All individualswere additionally genotyped for the multiple sclerosis associatedgenetic factors: HLA-DRB1*1501, rs2104286 (IL2RA) and rs6897932 (IL7R).

B. Results

In order to determine whether there is an association between geneticvariation and IL-21 production, we genotyped 73 subjects, in whompre-alemtuzumab serum IL-21 concentration had been determined, for foursingle nucleotide polymorphisms (SNPs) that lie within a block oflinkage disequilibrium (LD) on chromosome 4q27 encoding the IL-21 gene.The minor allele frequency for all four SNPs was in line with publisheddata: rs13151961G (14.5%), rs6822844T (14.6%), rs4833837G (38.0%) andrs6840978T (18.1%) (Glas et al., Am. J. Gastroenterol. 104, 1737-1744(2009)). We found that the genotype at 3 of the 4 SNPs (rs13151961 A/A,rs6822844 G/G and rs6840978 C/C) was associated with significantlyhigher levels of serum IL-21 (p values: 0.0076, 0.0098 and 0.0067respectively). The genotype at rs4833837 did not influence IL-21production. The LD between rs4833837 and the three other SNPs is low(r²<0.15), therefore a SNP which lies on the haplotypers13151961(A)-rs6822844(G)-rs6840978(C) is most likely to be associatedwith increased IL-21 production. The genotype frequencies forHLA-DRB1*1501, rs2104286 (IL2RA) and rs6897932 (IL7R) did not differfrom published data for other unselected patients with multiplesclerosis (International Multiple Sclerosis Genetics Consortium (IMSGC),Lancet Neurol. 7, 567-569 (2008); Yeo et al., Ann Neurol 61, 228-236(2007)).

Finally, in order to address whether genotype influences susceptibilityto autoimmunity after alemtuzumab, we categorized as many patients aspossible into those who did (27 subjects) and definitely did not (23subjects) develop autoimmunity post-alemtuzumab. 23 patients could notbe categorized due to transient autoantibody production and/orinsufficient time since exposure to alemtuzumab. The genotypes(rs13151961 A/A, rs6822844 G/G, rs6840978 C/C), shown to be associatedwith higher serum IL-21 concentration, were also found to be associatedwith autoimmunity after alemtuzumab.

1. A method for detecting elevated IL-21 level in a multiple sclerosis(MS) patient, comprising the steps of: obtaining a blood sample from anMS patient, measuring the IL-21 level in the blood sample, and comparingthe IL-21 level to the IL-21 level in a control blood sample from asubject without an autoimmune disease.
 2. A method for detecting singlenucleotide polymorphisms (SNPs) in a multiple sclerosis (MS) patient,comprising the steps of obtaining a DNA sample from an MS patient, andgenotyping the patient to detect the presence or absence of one or moregenotypes of single nucleotide polymorphisms (SNPs) selected from thegroup consisting of: A/A at SNP rs13151961, G/G at SNP rs6822844, andC/C at SNP rs6840978. 3-10. (canceled)
 11. A method for treating amultiple sclerosis (MS) patient, comprising the steps of: selecting anMS patient who has been diagnosed as being in need of heightenedmonitoring for development of a secondary autoimmune disease afterlymphocyte depleting therapy, wherein the need has been diagnosed by (i)measuring IL-21 in a blood sample from the patient, or (ii) determiningthe presence or absence of one or more genotypes of single nucleotidepolymorphisms (SNPs) selected from the group consisting of: A/A at SNPrs13151961, G/G at SNP rs6822844, and C/C at SNP rs6840978, whereinelevated IL-21 in said patient compared to a subject without anautoimmune disease or the presence of one or more of said SNPs indicatesthat the patient is in need of heightened monitoring for development ofa secondary autoimmune disease after lymphocyte depleting therapy,compared to MS patients without elevated IL-21 or without said SNPs;administering a therapeutic agent that targets CD52-bearing cells tosaid patient; and monitoring said patient for development of a secondaryautoimmune disease.
 12. (canceled)
 13. The method for claim 11, furthercomprising administering an IL-21 antagonist to the patient. 14.(canceled)
 15. A method for treating a multiple sclerosis (MS) patient,comprising the steps of: selecting a patient who has been diagnosed asnot being at increased risk of developing a secondary autoimmune diseaseafter lymphocyte depletion therapy, wherein the risk has been diagnosedby (i) measuring IL-21 in a blood sample from the patient, or (ii)determining the presence or absence of one or more genotypes ofsingle-nucleotide polymorphisms (SNPs) selected from the groupconsisting of: A/A at SNP rs13151961, G/G at SNP rs6822844 G/G, and C/Cat SNP rs6840978, wherein a normal IL-21 level compared to a subjectwithout an autoimmune disease or the absence of said SNPs indicates thatthe patient is not at increased risk of developing a secondaryautoimmune disease after lymphocyte depletion therapy, compared to MSpatients without elevated IL-21 or without said SNPs; and administeringa therapeutic agent that targets CD52-bearing cells to said patient.16-43. (canceled)
 44. The method of claim 11, wherein the measuring isof serum IL-21.
 45. (canceled)
 46. The method of claim 11, wherein thesecondary autoimmune disease is selected from the group consisting of:immune thrombocytopenic purpura (ITP), Graves' disease, Goodpasture'sdisease, autoimmune thyroid disease, autoimmune hemolytic anemia,autoimmune neutropenia, and autoimmune lymphopenia. 47-54. (canceled)55. The method of claim 11, wherein the blood sample is obtained fromthe patient prior to a lymphocyte depleting therapy.
 56. The method ofclaim 11, wherein the multiple sclerosis is relapsing-remitting multiplesclerosis, primary progressive multiple sclerosis, or secondaryprogressive multiple sclerosis. 57-58. (canceled)
 59. A method forassessing T cell responsiveness to treatment with a lymphocyte depletingtherapy in a multiple sclerosis patient, comprising: measuring caspase-3in T cells obtained from said patient after said therapy, wherein anincrease in caspase-3 in said T cells compared to T cells from an MSpatient not receiving said therapy is indicative of T cellresponsiveness to said therapy. 60-78. (canceled)
 79. A kit forperforming the method of claim 11, comprising: an anti-interleukin-21(IL-21) antibody and one or more reagents for detecting the binding ofsaid antibody to IL-21 in a blood sample from the MS patient; and/or oneor more reagents suitable for identifying the genotype of one or moresingle nucleotide polymorphisms (SNPs) selected from the groupconsisting of: SNP rs13151961, SNP rs6822844, and SNP rs6840978, in asample obtained from an individual; and a therapeutic agent that targetsCD52-bearing cells.
 80. (canceled)
 81. The method of claim 11, whereinthe therapeutic agent that targets CD52-bearing cells is an anti-CD52antibody or an antigen-binding portion thereof.
 82. The method of claim11, wherein the therapeutic agent that targets CD52-bearing cells isalemtuzumab.
 83. The method of claim 15, wherein the measuring is ofserum IL-21.
 84. The method of claim 15, wherein the secondaryautoimmune disease is selected from the group consisting of: immunethrombocytopenic purpura (ITP), Graves' disease, Goodpasture's disease,autoimmune thyroid disease, autoimmune hemolytic anemia, autoimmuneneutropenia, and autoimmune lymphopenia.
 85. The method of claim 15,wherein the blood sample is obtained from the patient prior to alymphocyte depleting therapy.
 86. The method of claim 15, wherein themultiple sclerosis is relapsing-remitting multiple sclerosis, primaryprogressive multiple sclerosis, or secondary progressive multiplesclerosis.
 87. The method of claim 15, wherein the therapeutic agentthat targets CD52-bearing cells is an anti-CD52 antibody or anantigen-binding portion thereof.
 88. The method of claim 15, wherein thetherapeutic agent that targets CD52-bearing cells is alemtuzumab.